Molecular mechanics dihedral angle

Snow, Amzel [316] contacts, and log P is log P R rotamer probabilities 15° increments in Molecular mechanics dihedral angles energy... 

You can often use experimental data, such as Nuclear Overhauser Effect (NOE) signals from 2D NMR studies, as restraints. NOE signals give distances between pairs of hydrogens in a molecule. Use these distances to limit distances during a molecular mechanics geometry optimization or molecular dynamics calculation. Information on dihedral angles, deduced from NMR, can also limit a conformational search. 

You can restrain atoms during molecular mechanics or quantum mechanics calculations. Choosing restraints, via the Restraint Forces dialog box, applies additional harmonic forces—which you specify, to interatomic distances, angles, or dihedrals that you have set up as named selections. 

Molecular mechanics (MM) calculations have been employed for determining dihedral angles and to establish a comparison with values calculated from coupling constants, during conformational studies of tricyclic and tetracyclic quinolizidine alkaloids. The MM results had to be treated with care, as they sometimes predicted ring conformations different to those supported by experimental data <1999JST215>. 

Figure 4.14 Results of molecular mechanics calculation. Main-chain dihedral angle dependence on the potential energy of (a) it- and si-(S)-3,7-dimethyloctyl-3-methylbutylsilane 31 repeat units with hydrogen termini (20), and (b) it- and si-(S)-3,7-dimethyloctyl-2-methyl-propylsilane 31 repeat units with hydrogen termini (21).

The idea that the most stable conformation of 42 and 43 may be helical is supported by a molecular mechanics calculation using Discover III with a PCFF force held (MSI, ver. 3.00). Figure 4.31a shows the total energy of a 42 oligomer with 21 Si repeat units as a function of the Si-Si-Si-Si dihedral angle. The respective P- and M-helical conformations of 42 near dihedral angles of 160° and 200° are more stable than a trans planar conformation of... 

For polymers with achiral substituents, molecular mechanics calculations (Discover 3, ver. 4.00 simple minimization) by us of potential energy as a function of dihedral angle afforded symmetrical multi-well-potential curves, with nonminimum 180° values, as shown in Figures 4.37a and 4.37b for H-(Ph2Si)3o-H and H-[(/7-n-BuPh)2Si]30-H, respectively. 

Semiempirical and molecular mechanics calculations have been widely used. Thus, conformation of indolo benzazepine 423 (Figure 8) with its conjugated benzo and indole rings has been studied by molecular mechanics (MMX force field). Its planarity was estimated from a calculation of dihedral angle Ti 2 3 4 the value of ca. 22° is due to strain as contributed by azepine ring. This characteristic was further compared to that of the open-chain and six-membered... 

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